Magnesium in PDB 6a1d: Crystal Structure of A Synthase 1 From Santalum Album in Complex with Ligand

Protein crystallography data

The structure of Crystal Structure of A Synthase 1 From Santalum Album in Complex with Ligand, PDB code: 6a1d was solved by X.Han, T.P.Ko, W.D.Liu, C.C.Chen, R.T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.94 / 1.78
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.437, 139.487, 110.930, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20.6

Other elements in 6a1d:

The structure of Crystal Structure of A Synthase 1 From Santalum Album in Complex with Ligand also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Synthase 1 From Santalum Album in Complex with Ligand (pdb code 6a1d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of A Synthase 1 From Santalum Album in Complex with Ligand, PDB code: 6a1d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6a1d

Go back to Magnesium Binding Sites List in 6a1d
Magnesium binding site 1 out of 2 in the Crystal Structure of A Synthase 1 From Santalum Album in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Synthase 1 From Santalum Album in Complex with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:29.9
occ:1.00
OAF A:6R2601 1.9 30.6 1.0
OAH A:6R2601 2.0 30.9 1.0
OD2 A:ASP316 2.0 25.1 1.0
OD2 A:ASP320 2.0 31.5 1.0
O A:HOH896 2.2 29.5 1.0
O A:HOH816 2.2 30.0 1.0
CG A:ASP316 2.9 23.9 1.0
MG A:MG603 3.0 29.2 1.0
CG A:ASP320 3.2 31.4 1.0
PAY A:6R2601 3.2 40.0 1.0
PAZ A:6R2601 3.2 37.5 1.0
OD1 A:ASP316 3.2 26.1 1.0
OAG A:6R2601 3.5 41.5 1.0
CB A:ASP320 3.7 31.0 1.0
CAX A:6R2601 3.8 41.4 1.0
CLK A:6R2601 4.1 41.6 1.0
O A:HOH958 4.1 36.4 1.0
OAT A:6R2601 4.2 38.8 1.0
OAI A:6R2601 4.2 38.5 1.0
OD1 A:ASP320 4.2 42.0 1.0
O A:HOH906 4.3 30.0 1.0
CB A:ASP316 4.3 24.6 1.0
O A:ASP316 4.4 23.7 1.0
OD1 A:ASP317 4.4 30.8 1.0
OAE A:6R2601 4.4 39.3 1.0
C A:ASP316 4.6 25.2 1.0
O A:HOH797 4.7 25.9 1.0
O A:HOH868 4.8 32.9 1.0
N A:ASP317 5.0 20.0 1.0

Magnesium binding site 2 out of 2 in 6a1d

Go back to Magnesium Binding Sites List in 6a1d
Magnesium binding site 2 out of 2 in the Crystal Structure of A Synthase 1 From Santalum Album in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Synthase 1 From Santalum Album in Complex with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:29.2
occ:1.00
OAH A:6R2601 2.0 30.9 1.0
OD2 A:ASP320 2.1 31.5 1.0
OD1 A:ASP316 2.1 26.1 1.0
O A:HOH797 2.2 25.9 1.0
O A:HOH906 2.2 30.0 1.0
O A:HOH868 2.2 32.9 1.0
CG A:ASP320 2.9 31.4 1.0
MG A:MG602 3.0 29.9 1.0
CG A:ASP316 3.0 23.9 1.0
OD1 A:ASP320 3.1 42.0 1.0
PAY A:6R2601 3.3 40.0 1.0
OD2 A:ASP316 3.4 25.1 1.0
OAE A:6R2601 3.5 39.3 1.0
OE2 A:GLU394 3.9 29.4 1.0
O A:HOH816 4.3 30.0 1.0
CLK A:6R2601 4.3 41.6 1.0
CB A:ASP320 4.3 31.0 1.0
OAG A:6R2601 4.3 41.5 1.0
CE1 A:TYR391 4.3 23.2 1.0
O A:HOH876 4.3 31.8 1.0
CB A:ASP316 4.4 24.6 1.0
CAX A:6R2601 4.4 41.4 1.0
CD1 A:TYR391 4.4 21.9 1.0
OAF A:6R2601 4.4 30.6 1.0
O A:ASP316 4.4 23.7 1.0
O A:HOH712 4.5 35.7 1.0
CA A:ASP316 4.8 21.4 1.0
O A:HOH896 4.8 29.5 1.0
C A:ASP316 4.9 25.2 1.0
CZ A:TYR391 5.0 19.9 1.0

Reference:

X.Han, T.P.Ko, W.D.Liu, C.C.Chen, R.T.Guo. Crystal Structure of A Synthase 1 From Santalum Album in Complex with Ligand To Be Published.
Page generated: Mon Dec 14 22:18:39 2020

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